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Records of the period, including Khan's origins, are vague. He was the product of a selective breeding or genetic engineering program, based on the eugenic philosophy that held improving the capabilities of a man improved the entire Human race. Augments produced by the program possessed physical strength and analytical capabilities considerably superior to ordinary Humans, and were created from a variety of Earth's ethnic groups. Khan's background was suspected to be Sikh, from the northern region of India.

Khan lived up to the axiom coined by one of his creators, "superior ability breeds superior ambition". By 1993, a wave of the genetic "supermen," including Khan, had simultaneously assumed control of more than forty of Earth's nations. From 1992 to 1996, Khan was absolute ruler of more than one-quarter of Earth's population, including regions of Asia and the Middle East. Considered "the best of tyrants", he severely curtailed the freedoms of his subjects, but his reign was an exception to similar circumstances in Earth history – lacking internal massacres or wars of aggression.

Khan aboard the Botany Bay

In the mid-1990s, the Augment tyrants began warring amongst themselves. Other nations joined in, to force them from power, in a series of struggles that became known as the Eugenics Wars. Eventually, most of the tyrants were defeated and their territory recaptured, but up to ninety "supermen" were never accounted for.

Following the destruction of Vulcan in 2258, AdmiralAlexander Marcus of Section 31 initiated a program to militarize Starfleet and began searching the galaxy for weapons to be used in the war with the Klingon Empire that he now believed was inevitable. Discovering the SS Botany Bay, Marcus brought Khan out of cryogenic suspension, believing his savage intellect would be a prime asset. He forced Khan into working with him by threatening to kill his fellow Augments, and set him to work designing weapons and ships for Starfleet, including the Dreadnought-classUSS Vengeance. Khan was recruited under the new identity of John Harrison.

Disgruntled, Harrison tried to smuggle his crew away in advanced long-range torpedoes but was discovered and forced to flee alone. Believing Marcus had killed his crew, he coerced Section 31 agent Thomas Harewood into betraying Starfleet by offering a blood transfusion for Harewood's terminally-ill daughter. Harewood agreed, and Harrison replaced his Starfleet Academy ring with a bomb. After his daughter was cured with a vial of Harrison's blood and its regenerative platelets, Harewood went to work at his office in the Kelvin Memorial Archive in London, where he dropped the false Starfleet ring into a glass of water, igniting the bomb and destroying the facility. In the midst of the chaos, Harrison used the opportunity to inspect a salvaged terminal to gain the confiscated formula for transwarp beaming.

Harrison piloting Jumpship 208

Before he set off the explosion, Harewood sent Marcus a message, explaining he had been threatened by Harrison. Knowing that Marcus would call an emergency meeting in the light of the bombing, Harrison rigged a combat efficient jumpship with a portable transwarp beaming device and headed to the meeting location. Once the conference was underway, Harrison appeared and laid waste to the conference, killing Admiral Pike, Captain Abbott and many other high ranking Starfleet officers. James T. Kirk disabled the jumpship, but Harrison beamed himself away before it crashed. He arrived in the one place Starfleet could not go: Qo'noS, the Klingon homeworld.

"John Harrison" reveals himself on Qo'noS

Undeterred, Kirk was granted permission by Admiral Marcus to travel to Qo'noS and fire 72 experimental photon torpedoes on Harrison's location. However, at the behest of his crew, Kirk chose to defy his orders and opted to arrest Harrison instead. While Kirk led an away team with Spock, Uhura, and Hendorff, acting captainSulu transmitted a message to Harrison, warning him to surrender or be destroyed by the shipboard torpedoes. Harrison found Kirk, Spock, and Uhura being attacked by a Klingon patrol and single-handedly killed dozens of Klingons. Confronting the landing party, Harrison asked how many torpedoes the Enterprise had on board. Spock informed him of the count, which corresponded exactly to the number of his former crew members which were still in stasis. Harrison then surrendered to the landing party. Kirk, angry that his mentor's murderer had saved them, punched Harrison repeatedly but was unable to render him unconscious.

Khan in custody

From the brig, Leonard McCoy took a blood sample to analyze the secret behind Harrison's superhuman strength and abilities and injected it into a dead tribble. Harrison refused to answer Kirk's questions; he instead gave him coordinates to the spacedock near Jupiter where the Vengeance was constructed, and suggested he open one of the experimental torpedoes. Kirk gave the coordinates for the absent Montgomery Scott to investigate, while McCoy and Marcus's daughter Carol opened up a torpedo and discovered a cryogenically frozen man within. Khan finally explained who he was to Kirk, and revealed that the torpedoes contained his fellow surviving Augments as part of a cover-up. Admiral Marcus appeared in the Vengeance and demanded Kirk hand over Khan. Kirk refused, and the Enterprise warped back to Earth so Khan could be brought to trial. The Vengeance caught up in subspace and fired on the Enterprise as it arrived outside Earth.

Kirk and Khan team up

Marcus beamed his daughter over to the Vengeance and prepared to destroy the Enterprise but Scott, who had snuck aboard the Vengeance at its spacedock, deactivated its weapons. Kirk and Khan donned thruster suits to fly over and commandeer the Vengeance. Meanwhile, Spock consulted his older counterpart from another timeline regarding whether he ever encountered Khan Noonien Singh: the old Spock responded he had, that he was dangerous, and that it had required a great sacrifice to stop him. Kirk had grown suspicious of Khan and advised Scott to stun him once they had taken over the bridge of the Vengeance.

When they arrived on the bridge, Scott shot Khan while Kirk admonished Marcus for compromising the Federation. This did not subdue Khan, who flung himself at Scott and Kirk, overpowered them and broke Carol's leg before crushing her father's skull with his bare hands. Khan then sat in the command chair and ordered Spock to hand over the torpedoes or he would kill Kirk and resume bombarding the Enterprise. Spock obliged, and Khan beamed Kirk, Scott and Carol back into the Enterprise's brig, but reneged on the deal. Spock, having predicted Khan's betrayal, had ordered McCoy to remove the stasis pods and detonated the torpedoes, crippling the Vengeance. Khan cried out in anguish at the apparent loss of his crew.

Khan sets the Vengeance on a course with the heart of Starfleet

The damage sustained caused both ships to be drawn by Earth's gravitational pull. To prevent the ship crashing into western North America, Kirk sacrificed himself reactivating the ship's warp core. Khan, on the other hand, directed the Vengeance on a crash course for Starfleet Headquarters, though the computer could not guarantee that Khan would make it. The Vengeance slammed into the old prison on Alcatraz Island, careened across San Francisco Bay, and then plowed into several buildings, demolishing several skyscrapers. When the Vengeance crashed into the city, Khan leapt off the bridge and posed as a shocked survivor. Spock beamed down to execute Khan and avenge Kirk's death, pursuing him onto automated flying barges. The chase ends in a climatic hand-to-hand fight, where Khan comes close several times to killing Spock. In the Enterprise's medbay, McCoy had just examined Kirk's body when the dead tribble on his desk came back to life.

Khan in stasis following his defeat

Spock attempted to subdue Khan with a nerve pinch and then a mind meld, but to no avail. Uhura beamed down, firing several stun shots to weaken Khan and revealed to Spock that they needed Khan alive to save Kirk. Spock finally knocked Khan out. After his blood was used to revive Kirk, Khan was placed back in suspended animation with his crew from the Botany Bay. (Star Trek Into Darkness)

"Alexander Marcus needed to respond to an uncivilized threat in a civilized time, and for that, he needed a warrior's mind - my mind - to design weapons and warships."'"You are suggesting the Admiral violated every regulation he vowed to uphold, simply because he wanted to exploit your intellect.""He wanted to exploit my savagery! Intellect alone is useless in a fight, Mr. Spock. You, you can't even break a rule; how can you be expected to break bone?"

- Khan and Spock

"Marcus used me to design weapons to help him realize his vision of a militarized Starfleet. He sent you to use those weapons; to fire my torpedoes on an unsuspecting planet, and then he purposely crippled your ship in enemy space, leading to one inevitable outcome: the Klingons would come searching for whomever was responsible, and you would have no chance of escape. Marcus would finally have the war he talked about, the war he always wanted."

- Khan, revealing Marcus' plans and intentions to Kirk and Spock

"I watched you open fire in a room full of unarmed Starfleet officers. You killed them in cold blood.""Marcus took my crew from me...""You are a murderer!""He used my friends to control me. I tried to smuggle them to safety by concealing them in the very weapons I had designed. But I was discovered. I had no choice but to escape alone. And when I did, I had every reason to suspect that Marcus had killed every single one of the people I hold most dear! So I responded in kind."

- Kirk and Khan

"My crew... is my family, Kirk. Is there anything you would not do... for your family?"

- Khan to Kirk, trying to justify his actions

"If you think you're safe at warp, you're wrong."

- Khan to Carol Marcus, shortly before the Vengeance fires on the Enterprise in subspace

"You... You should have let me sleep!"

- Khan to Alexander Marcus before crushing his skull.

"Well, let's play this out logically then, Mr. Spock. First, I will kill your captain to demonstrate my resolve, then if yours holds I will have no choice but to kill you and your entire crew."
"If you destroy our ship, you will also destroy your own people."
"Your crew requires oxygen to survive, mine does not. I will target your life support systems located behind the aft nacelle. And after every single person aboard your ship suffocates I will walk over your cold corpses to recover my people. Now...shall we begin?"

Bringing back Khan Noonien Singh was discussed before the release of Star Trek; on the film's audio commentary, it is stated the filmmakers considered having a shot of the SS Botany Bay after the credits, but opted out in case they decided not to use the character. Director J.J. Abrams said, "It'll be fun to hear what Alex and Bob are thinking about Khan. The fun of this timeline is arguing that different stories, with the same characters, could be equally if not more compelling than what's been told before [....] Certain people are destined to cross paths and come together, and Khan is out there... even if he doesn't have the same issues." [1]

Co-writer Damon Lindelof said the jumping-off point for the sequel's story was deciding whether Khan would be the villain, and he, Kurtzman and Orci weighed the pros and cons of using the character. [2] Abrams commented that, in comparison to Nero from Star Trek, the writers wanted "a much more nuanced and complex villain" for Into Darkness. (Cinefex, No. 134, p. 72) Due to the massive popularity of how Khan had been represented before, however, "there was a good year of debate," explained Alex Kurtzman, over whether to include Khan in the upcoming movie. With a laugh, Orci phrased this issue, "To Khan or not to Khan." Kurtzman observed, "The choice to play in that sandbox is really complicated because when a character was as beloved as Khan, you really have to have a reason to do it." [3] During the debate, Lindelof wanted to use Khan, while Orci was against this option.

The filmmakers found a compromise by developing a story that would not entail Khan, and then determining if he could be "reverse engineered" into it. [4] Stated Kurtzman, "If we could take that [tale] and then incorporate Khan into the mix in a way that felt reverent and appropriate for that story, we would do it. Without that standard, we wouldn't […] We all loved the 'Space Seed' back story, the idea that he was a man who loved his crew as his family — that was the understandable and relatable agenda. And then we built outward from there." [5]
Eventually, Orci felt "the details became too juicy to avoid. Genetic super man from a time that understood war and savagery, etc. Once we had a basic structure that did not necessarily necessitate him, we were able to tailor the script itself to details and inspirations that he brought." [6] Lindelof added the storyline avoided "The audience [knowing] something the bridge crew did not, which was 'Whatever you do, don’t wake that dude up.' So we didn't want to put the bridge crew behind the audience in terms of what they knew about Trek." [7]

Khan's undercover name was inspired by his name in an early draft of the script for "Space Seed", John Ericssen. Orci said, "We shot the movie using the name Ericsenn [sic] but decided it would give it away[,] so we cheated the name Harrison into everyone's mouth!" [8] According to John Eaves, the character's production codename was April, another character Orci said he had considered as a villain. [9][10] Once they chose to bring Khan into their film, the screenwriters were not necessarily eager to additionally incorporate a moment when the character's name is shouted in anger, as happens in Star Trek II: The Wrath of Khan, because they condidered it vital that such a reaction be a natural and realistic one. [11]

Khan was portrayed by Benedict Cumberbatch. Before he was cast, Abrams approached Benicio del Toro for the role. [12] Orci said they shyed away from casting an Asian actor as Khan because "it became uncomfortable for me to support demonizing anyone of color, particularly any one of middle eastern descent or anyone evoking that. One of the points of the movie is that we must be careful about the villain within US, not some other race." He also stated the "true essence" of Khan's character was "that he was a genetically engineered superman," "not where he was from or the color of his skin." [13] In response to a question asking whether Khan's appearance was "cosmetically altered to avoid detection," Orci said that the theory was an "interesting idea. Could be."[14] Also, in answer to a question about Khan's change in features, Orci stated, "Uhm…. one of his abilities is that he is a shape shifter?"[15]

Cumberbatch commented the role was "daunting because of the legacy involved and the amount of speculation about [Khan] possibly being the villain." (Empire issue 289, p. 23) Lindelof said of writing for Cumberbatch that "when you can get [a] monologue to come out of [his] mouth, does the 'writing' even matter? I mean, seriously, I made that guy say 'Milk, milk lemonade, and this is where the fudge is made' and it scared the living shit out of me." [16]

Cumberbatch was cast two weeks before filming. Mary L. Mastro, head of the film's hair department, wanted Khan to have black hair to contrast with the blond Kirk. She recalled, "JJ called a meeting with the creators involved in what he was going to look like and [Cumberbatch] walks into the room with super-short blond hair. My mouth dropped open, like, 'Oh, great.'" The schedule was altered slightly to give more time to determine Cumberbatch's appearance in the film. [17] The filmmakers considered giving Cumberbatch a shoulder-length wig, but Abrams felt he looked better without it. (Star Trek Into Darkness iTunes enhanced commentary) Costume Designer Michael Kaplan wanted Khan to be "dapper," giving him "a number of very long, elegant coats. It's nice, even in the distance, to be able to recognise a character right away. He's pretty high fashion-looking."

Cumberbatch trained one-to-one with his stunt double, Martin De Boer, learning basic martial arts. De Boer described Cumberbatch as "'very receptive to learning. I've had actors who want to be an action star but don't want to put in the work, and he was the opposite, he said, 'I want to train as much as I can.' He was very committed. Besides working with us, he was working with his personal trainer five, six days a week; he really got in shape." De Boer said that, because of Khan's strength, Cumberbatch "wanted to have more static and powerful movements. That strength changes the rules of the martial arts we use. You don't have to do five punches, you just have to use a couple of moves and he takes out the guy already." [18]

Bad Robot Productions went to great lengths to hide Khan's identity, even screening the space jump scene to the press with life sign readouts displayed as "Harrison" and Spock's lines referring to Khan overdubbed to refer to Harrison. Bryan Burk defended the strategy, stating, "Even if you don't even know who Khan is, you know that you're watching a film where for forty-five minutes or an hour of the movie you are ahead of the characters. So you're just kind of waiting for them to catch up with what you already know, that he is not who he says he is." [19] Cumberbatch said the secrecy was fine for him, though Alice Eve did tease him, saying, "The lies, Benedict, the lies!" Recalling times when he had sneaked into screenings to see the audience's reaction to Khan revealing himself, Cumberbatch remarked that "to have that moment – that's worth any amount of subterfuge or holding back on reveals." (Empire issue 289, p. 23)

The creative staff were ultimately very pleased with how Khan is depicted in Into Darkness. "Ultimately, I think we felt that we found a reason and a way to do it that was all of the things we needed it to be, and yet really different," voiced Kurtzman. "I think the mistake that we could have made, that we didn't want to make, was to do a version of what Ricardo Montalban had done so brilliantly, and then fall short of that […] There are things about Khan that are very familiar, and there are things that are entirely different, and that's exactly what we wanted to do." [20]

However, Abrams voiced regret over keeping Khan's identity a secret. "The truth is I think it probably would have been smarter just to say upfront 'This is who it is.' It was only trying to preserve the fun of it, and it might have given more time to acclimate and accept that's what the thing was," he said. He added that hiding Khan's presence was mandated by the studio, who did not want to alienate non-Star Trek fans with the impression they had to learn about who Khan was to enjoy the film. Abrams agreed with that notion but "wonder[ed] if it would have seemed a little bit less like an attempt at deception if we had just come out with it." [21] Responding to Burk's comment that it might have hurt the film if the audience knew Harrison was Khan before Kirk did, Abrams added "the truth is it probably wouldn't have made much of a difference in that regard." [22]

When asked if Cumberbatch could reprise the role, Lindelof replied, "To answer that question would be to determine whether or not he actually survives this movie, but if he survives this movie, we would be incredibly stupid to not use him again." [23] As to whether Khan's blood could disrupt dramatic tension in the next film, Orci said they "figured there are so many horrible ways to die in space that no medicine could save you from that we would be okay." [24]

Cumberbatch also portrayed Khan / Harrison in three "Disruptions" videos to promote the film, in which he analyzes Kirk, Spock, and Uhura's weaknesses and declares he will threaten them. [25]

According to his biography on the Star Trek movie app, 'John Harrison' was born in 2228 in Dover, Great Britain, Earth to Richard and Sara Harrison. Harrison was one of nine survivors of the attack on the colony on Tarsus IV in 2246, where both of his parents were killed in the attack. He graduated from the London School of Economics in 2250.

After graduating, he was appointed associate researcher, Starfleet Data Archive (London), East Annex in 2255. He was tasked with collection, organization and analysis of declassified data received from Starfleet commissioned starships and from Federation member states.

The comic book series Star Trek: Khan establishes Khan's history subsequent to the divergence of the timeline but prior to his encounter with the Enterprise. The Section 31 starship Vanguard discovers the Botany Bay and takes custody of Khan. Quickly using their databanks to determine his identity prior to awakening him, Admiral Marcus orders that Khan's face and voice be reconstructed from their Indian origins to a more northern European origin and has his memory blocked with the intent of convincing Khan that he is John Harrison, a Starfleet researcher in London's Kelvin Memorial Archive, who lost his memories in an accident during a failed mission to Qo'nos. He is given the task of helping advise Section 31 on possible enhancements to Starfleet weapon, shield and propulsion technology (which is to be incorporated aboard the USS Vengeance) as well as taking on a mission to destroy Praxis with the help of a portable transporter he designed and built. The mission is a success (explaining the destroyed moon seen in orbit of the Klingon homeworld in the film), but, in the process, Khan rediscovers his memories of his true identity. Discovering that his crew is being held in the London facility and forging transmissions from Marcus, Khan is able to load his crew into the long-range torpedoes with the intent of stealing a starship with them aboard, but, before departing, Khan invades Marcus' home and demands to know the truth before planning to kill him. The admiral, planning for Khan's rediscovery, has him targeted by a jumpship outside the window, forcing Khan to flee. His plan, now circumvented, forces him to coerce Thomas Harewood into destroying the London facility and set the events of the film into motion.

Star Trek: Khan also establishes that he was originally an ordinary Indian boy named Noonien Singh and was an orphan living in an impoverished New Delhi slum. In 1972, he was captured, along with other impoverished children, and taken to a research facility to be a test subject for genetic engineering experiments. In August 1985, as a young man, he escapes from the research facility, along with the other genetically engineered test subjects, and begins a rebellion. He later gives himself the title of "Khan" out of admiration for the historical Mongol conqueror Genghis Khan, naming himself Khan Noonien Singh.

Entertainment Weekly saw parallels between the new Khan and figures such as Osama Bin Laden or Saddam Hussein, as both men were allied with the US before turning on them. [26]Simon Pegg commented "Iraq had nothing proven to do with 9/11, and yet Bush used that as an excuse to start a war with those people. You can always see the Klingons as like Iraq and John Harrison the proxy for Osama bin Laden." [27]

Lindelof further acknowledged the terrorism parallels in an interview with StarTrek.com, as Khan's 72 torpedoes reminded them of the notion of 72 virgins in paradise. Lindelof responded "Of course it is a coincidence, because that is a number taken from canon. It was pointed out to us at the scripting phase – the 72 virgins – and that actually gave us pause, because we didn't want people drawing that comparison... but there it is." [28]